Differential Expression
Wald Tests
Light(Ab) vs Control(WT)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 543Is A-Beta-Cry2-mCh significantly differentially expressed?:
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | gene_biotype | external_gene_name | |
|---|---|---|---|---|---|---|---|---|
| A-Beta-Cry2-mCh | 326.8102 | 0.1830931 | 0.4401487 | 0.41598 | 0.6774246 | 0.8994422 | NA | NA |
##
## N U1 U2 U3 D3 D2 D1
## 9327 128 80 70 64 77 124
Wnt(Wg) vs. Control(WT)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 1049Is A-Beta-Cry2-mCh significantly differentially expressed?:
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | gene_biotype | external_gene_name | |
|---|---|---|---|---|---|---|---|---|
| A-Beta-Cry2-mCh | 326.8102 | -10.75238 | 1.256863 | -8.554939 | 0 | 0 | NA | NA |
##
## N U1 U2 U3 D3 D2 D1
## 8817 365 100 56 82 122 324
Wnt_Light(Wg_Ab) vs. Control(WT)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 1068Is A-Beta-Cry2-mCh significantly differentially expressed?:
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | gene_biotype | external_gene_name | |
|---|---|---|---|---|---|---|---|---|
| A-Beta-Cry2-mCh | 326.8102 | 1.252949 | 0.4911453 | 2.551075 | 0.0107391 | 0.0724138 | NA | NA |
##
## N U1 U2 U3 D3 D2 D1
## 8800 345 106 68 81 127 341
Wnt(Wg) vs. Light(Ab)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 996Is A-Beta-Cry2-mCh significantly differentially expressed?:
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | gene_biotype | external_gene_name | |
|---|---|---|---|---|---|---|---|---|
| A-Beta-Cry2-mCh | 326.8102 | -10.93548 | 1.256597 | -8.702451 | 0 | 0 | NA | NA |
##
## N U1 U2 U3 D3 D2 D1
## 8870 296 99 50 88 135 328
Wnt_Light(Wg_Ab) vs Light(Ab)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 1118Is A-Beta-Cry2-mCh significantly differentially expressed?:
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | gene_biotype | external_gene_name | |
|---|---|---|---|---|---|---|---|---|
| A-Beta-Cry2-mCh | 326.8102 | 1.069856 | 0.4904657 | 2.181306 | 0.0291608 | 0.1326898 | NA | NA |
##
## N U1 U2 U3 D3 D2 D1
## 8751 290 120 62 138 177 331
Wnt_Light(Wg_Ab) vs. Wnt(Wg)
Number of significant genes (padj < 0.1 & log2FoldChange < log2(1.5)):
## [1] 178Is A-Beta-Cry2-mCh significantly differentially expressed?:
| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | gene_biotype | external_gene_name | |
|---|---|---|---|---|---|---|---|---|
| A-Beta-Cry2-mCh | 326.8102 | 12.00533 | 1.275355 | 9.413327 | 0 | 0 | NA | NA |
##
## N U1 U2 U3 D3 D2 D1
## 9690 76 22 12 12 20 36
Likelihood Ratio Test
Number of significant genes (padj < 0.1):
## [1] 2801Session Info
## R version 4.0.5 (2021-03-31)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] forcats_0.5.1 stringr_1.4.0
## [3] dplyr_1.0.5 purrr_0.3.4
## [5] readr_1.4.0 tidyr_1.1.3
## [7] tibble_3.1.0 tidyverse_1.3.0
## [9] limma_3.46.0 geneplotter_1.68.0
## [11] annotate_1.68.0 XML_3.99-0.6
## [13] reshape_0.8.8 lattice_0.20-41
## [15] ggplot2_3.3.3 gridExtra_2.3
## [17] biomaRt_2.46.3 gplots_3.1.1
## [19] RColorBrewer_1.1-2 GenomicFeatures_1.42.3
## [21] AnnotationDbi_1.52.0 knitr_1.31
## [23] DESeq2_1.30.1 SummarizedExperiment_1.20.0
## [25] Biobase_2.50.0 MatrixGenerics_1.2.1
## [27] matrixStats_0.58.0 GenomicRanges_1.42.0
## [29] GenomeInfoDb_1.26.7 IRanges_2.24.1
## [31] S4Vectors_0.28.1 BiocGenerics_0.36.0
##
## loaded via a namespace (and not attached):
## [1] colorspace_2.0-0 ellipsis_0.3.1 rprojroot_2.0.2
## [4] XVector_0.30.0 fs_1.5.0 rstudioapi_0.13
## [7] farver_2.1.0 bit64_4.0.5 fansi_0.4.2
## [10] lubridate_1.7.10 xml2_1.3.2 splines_4.0.5
## [13] cachem_1.0.4 jsonlite_1.7.2 Rsamtools_2.6.0
## [16] broom_0.7.6 dbplyr_2.1.1 compiler_4.0.5
## [19] httr_1.4.2 backports_1.2.1 assertthat_0.2.1
## [22] Matrix_1.3-2 fastmap_1.1.0 cli_2.4.0
## [25] htmltools_0.5.1.1 prettyunits_1.1.1 tools_4.0.5
## [28] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.4
## [31] rappdirs_0.3.3 Rcpp_1.0.6 cellranger_1.1.0
## [34] jquerylib_0.1.3 vctrs_0.3.7 Biostrings_2.58.0
## [37] rtracklayer_1.50.0 xfun_0.22 rvest_1.0.0
## [40] lifecycle_1.0.0 gtools_3.8.2 zlibbioc_1.36.0
## [43] scales_1.1.1 hms_1.0.0 yaml_2.2.1
## [46] curl_4.3 memoise_2.0.0 sass_0.3.1
## [49] stringi_1.5.3 RSQLite_2.2.6 highr_0.8
## [52] genefilter_1.72.1 caTools_1.18.2 BiocParallel_1.24.1
## [55] rlang_0.4.10 pkgconfig_2.0.3 bitops_1.0-6
## [58] evaluate_0.14 labeling_0.4.2 GenomicAlignments_1.26.0
## [61] bit_4.0.4 tidyselect_1.1.0 plyr_1.8.6
## [64] magrittr_2.0.1 R6_2.5.0 generics_0.1.0
## [67] DelayedArray_0.16.3 DBI_1.1.1 pillar_1.6.0
## [70] haven_2.3.1 withr_2.4.1 survival_3.2-10
## [73] RCurl_1.98-1.3 modelr_0.1.8 crayon_1.4.1
## [76] KernSmooth_2.23-18 utf8_1.2.1 BiocFileCache_1.14.0
## [79] rmarkdown_2.7 progress_1.2.2 locfit_1.5-9.4
## [82] readxl_1.3.1 blob_1.2.1 reprex_2.0.0
## [85] digest_0.6.27 xtable_1.8-4 openssl_1.4.3
## [88] munsell_0.5.0 bslib_0.2.4 askpass_1.1